10-93926824-C-G

Variant names:

• chr10-93926824-C-G
• rs829237
• ENST00000605679.5:n.*253+14025C>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000605679.5(SLC35G1):​n.*253+14025C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.483 in 151,998 control chromosomes in the GnomAD database, including 18,481 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.48 (18481 hom., cov: 32)
• Consequence: SLC35G1 ENST00000605679.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.900
• Publications: 1 publications found

Genes affected

SLC35G1 (HGNC:26607): (solute carrier family 35 member G1) This gene encodes a transmembrane protein which is a member of the drug/metabolite transporter protein superfamily. The encoded protein may play a role in the regulation of calcium levels inside the cell. [provided by RefSeq, Sep 2016]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.51).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.924 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000605679.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC35G1	ENST00000605679.5	TSL:1	n.*253+14025C>G		intron	N/A	ENSP00000474890.1
	SLC35G1	ENST00000494992.5	TSL:5	n.*253+14025C>G		intron	N/A	ENSP00000474294.1

Frequencies

GnomAD3 genomes AF: 0.483 AC: 73423 AN: 151880 Hom.: 18472 Cov.: 32

Gnomad AFR AF: 0.442

Gnomad AMI AF: 0.462

Gnomad AMR AF: 0.503

Gnomad ASJ AF: 0.453

Gnomad EAS AF: 0.945

Gnomad SAS AF: 0.570

Gnomad FIN AF: 0.521

Gnomad MID AF: 0.415

Gnomad NFE AF: 0.460

Gnomad OTH AF: 0.448

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.483 AC: 73474 AN: 151998 Hom.: 18481 Cov.: 32 AF XY: 0.490 AC XY: 36378 AN XY: 74288

African (AFR) AF: 0.442 AC: 18326 AN: 41442

American (AMR) AF: 0.503 AC: 7680 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.453 AC: 1570 AN: 3468

East Asian (EAS) AF: 0.946 AC: 4897 AN: 5178

South Asian (SAS) AF: 0.569 AC: 2740 AN: 4816

European-Finnish (FIN) AF: 0.521 AC: 5498 AN: 10552

Middle Eastern (MID) AF: 0.408 AC: 120 AN: 294

European-Non Finnish (NFE) AF: 0.460 AC: 31276 AN: 67958

Other (OTH) AF: 0.449 AC: 948 AN: 2112

Alfa AF: 0.460 Hom.: 1978

Bravo AF: 0.481

Asia WGS AF: 0.730 AC: 2537 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.51
CADD	Benign	16
DANN	Benign	0.78
PhyloP100		0.90

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs829237; hg19: chr10-95686581;